Variant report

Variant	rs6829705
Chromosome Location	chr4:48379333-48379334
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48341542..48343650-chr4:48378558..48381453,2	K562	blood:

Variant related genes	Relation type
ENSG00000109171	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10003230	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10026398	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10029785	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10805168	0.88[ASN][1000 genomes]
rs1117010	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12503644	0.84[ASN][1000 genomes]
rs12507206	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12511991	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12645951	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12649527	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12649528	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13105385	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13115295	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13133788	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13148849	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13150017	0.86[EUR][1000 genomes]
rs1352433	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1352434	0.86[ASN][1000 genomes]
rs1472967	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1586540	0.90[ASN][1000 genomes]
rs1703973	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1948167	0.90[ASN][1000 genomes]
rs2029348	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2291474	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291475	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2353312	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2353314	0.86[ASN][1000 genomes]
rs2353315	0.81[ASN][1000 genomes]
rs28409655	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34975258	0.81[ASN][1000 genomes]
rs35758434	0.90[ASN][1000 genomes]
rs372825	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs382335	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3828496	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs404348	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs404445	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs404656	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs411261	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs421336	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs421833	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs429969	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs432927	0.83[EUR][1000 genomes]
rs445892	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs449376	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs450498	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4694895	0.90[ASN][1000 genomes]
rs62309425	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6447634	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6447635	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6816010	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6816352	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6821277	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6836010	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6837335	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6844211	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6848073	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6848395	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7438704	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7668529	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7672892	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7674269	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7678164	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7700018	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs923372	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs923373	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9291323	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs974014	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs974015	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs974016	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9996532	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6829705	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48355000-48380000	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr4:48355000-48412600	Weak transcription	Aorta	Aorta
3	chr4:48355200-48379800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:48355800-48390600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr4:48357200-48384600	Weak transcription	Lung	lung
6	chr4:48359200-48384400	Weak transcription	Fetal Muscle Leg	muscle
7	chr4:48361000-48384600	Weak transcription	Fetal Stomach	stomach
8	chr4:48362600-48384600	Weak transcription	Left Ventricle	heart
9	chr4:48363000-48380000	Weak transcription	Fetal Lung	lung
10	chr4:48363000-48384600	Weak transcription	Ovary	ovary
11	chr4:48363400-48405400	Weak transcription	Right Ventricle	heart
12	chr4:48363600-48382600	Weak transcription	Fetal Brain Male	brain
13	chr4:48363600-48382800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr4:48364000-48381400	Weak transcription	Fetal Heart	heart
15	chr4:48364200-48381800	Weak transcription	Adipose Nuclei	Adipose
16	chr4:48368600-48384600	Weak transcription	Thymus	Thymus
17	chr4:48368800-48384600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr4:48369600-48382600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:48371400-48395400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr4:48371600-48379600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr4:48372000-48379600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr4:48372000-48380600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr4:48372000-48384200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr4:48372200-48380800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:48372600-48380000	Weak transcription	Brain Angular Gyrus	brain
26	chr4:48372600-48387000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr4:48372600-48426800	Weak transcription	Small Intestine	intestine
28	chr4:48372800-48379600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr4:48372800-48379800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr4:48372800-48380000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr4:48372800-48380600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr4:48372800-48381000	Weak transcription	Fetal Brain Female	brain
33	chr4:48372800-48381400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr4:48372800-48381800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr4:48372800-48382000	Weak transcription	GM12878-XiMat	blood
36	chr4:48372800-48382600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr4:48372800-48384600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr4:48373000-48379800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr4:48373000-48379800	Weak transcription	Brain Hippocampus Middle	brain
40	chr4:48373000-48380000	Weak transcription	Brain Anterior Caudate	brain
41	chr4:48373000-48380400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:48373000-48380600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr4:48373000-48381400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr4:48373000-48381600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr4:48373000-48381600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr4:48373000-48384400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr4:48373000-48384800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr4:48373200-48379800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr4:48373200-48381800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:48374000-48379600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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